Below, we first show an aggregation of the latest version of FNGS for our respective post-processing pipelines:

  require(Discriminability)
## Loading required package: Discriminability
  signal_overall <- c()
  ids_overall <- c()
  cpac_graphs_overall <- c()
  cpac_ids_overall <- c()
  dataset_overall <- c()

FNGS

BNU1

  require(Discriminability)
  inpath <- 'C:/Users/ebrid/Documents/R/fngs_merge/BNU1/roi_timeseries/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 3
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal_overall, signal)
  ids_overall <- c(ids_overall, tsobj$dataset)
  
  cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/BNU1/FSL_frf_nsc_ngs_des/'
  cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
  scan_pos = 2
  cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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  cpac_graphs <- cpac_graobj[[1]]
  cpac_ids <- cpac_graobj[[3]]
  
  cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
  ids_overall <- c(ids_overall, cpac_graobj$dataset)

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))
## Warning: package 'reshape2' was built under R version 3.3.3
## Warning: package 'ggplot2' was built under R version 3.3.3

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

CPAC Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)
## [1] "computing hellinger distances and densities..."

  print(td$combinedplot)
## NULL

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)
## NULL

CPAC Raw Correlation Graphs

  cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_td$combinedplot)
## NULL

CPAC Ranked Correlation Graphs

  cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_tdr$combinedplot)
## NULL
  collection <- data.frame(dataset='BNU1',
                                             postprocessing=c('fngs_corr', 'fngs_rcorr',
                                                              'cpac_corr', 'cpac_rcorr'),
                           discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d))

DC1

  inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0503/DC1/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 2
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal_overall, signal)
  ids_overall <- c(ids_overall, tsobj$dataset)

  cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/DC1/FSL_frf_nsc_ngs_aal/'
  cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
  scan_pos = 2
  cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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  cpac_graphs <- cpac_graobj[[1]]
  cpac_ids <- cpac_graobj[[3]]
  
  cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
  ids_overall <- c(ids_overall, cpac_graobj$dataset)

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

CPAC Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)
## [1] "computing hellinger distances and densities..."

  print(td$combinedplot)
## NULL

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)
## NULL

CPAC Raw Correlation Graphs

  cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_td$combinedplot)
## NULL

CPAC Ranked Correlation Graphs

  cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_tdr$combinedplot)
## NULL
  collection <- rbind(collection, data.frame(dataset='DC1',
                                             postprocessing=c('fngs_corr', 'fngs_rcorr',
                                                              'cpac_corr', 'cpac_rcorr'),
                           discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d)))

HNU1

  inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0503/HNU1/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 2
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal_overall, signal)
  ids_overall <- c(ids_overall, tsobj$dataset)

  cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/HNU1/FSL_frf_nsc_ngs_aal/'
  cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
  scan_pos = 2
  cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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  cpac_graphs <- cpac_graobj[[1]]
  cpac_ids <- cpac_graobj[[3]]
  
  cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
  ids_overall <- c(ids_overall, cpac_graobj$dataset)

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

CPAC Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)
  print(td$combinedplot)

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)
## NULL

CPAC Raw Correlation Graphs

  cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_td$combinedplot)
## NULL

CPAC Ranked Correlation Graphs

  cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_tdr$combinedplot)
## NULL
  collection <- rbind(collection, data.frame(dataset='HNU1',
                                             postprocessing=c('fngs_corr', 'fngs_rcorr',
                                                              'cpac_corr', 'cpac_rcorr'),
                           discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d)))

NYU1

  inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0503/NYU1/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 2
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal_overall, signal)
  ids_overall <- c(ids_overall, tsobj$dataset)

  cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/NYU1/FSL_frf_nsc_ngs_aal/'
  cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
  scan_pos = 2
  cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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  cpac_graphs <- cpac_graobj[[1]]
  cpac_ids <- cpac_graobj[[3]]
  
  cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
  ids_overall <- c(ids_overall, cpac_graobj$dataset)

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

CPAC Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)
## [1] "computing hellinger distances and densities..."

  print(td$combinedplot)
## NULL

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)
## NULL

CPAC Raw Correlation Graphs

  cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_td$combinedplot)
## NULL

CPAC Ranked Correlation Graphs

  cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_tdr$combinedplot)
## NULL
  collection <- rbind(collection, data.frame(dataset='NYU1',
                                             postprocessing=c('fngs_corr', 'fngs_rcorr',
                                                              'cpac_corr', 'cpac_rcorr'),
                           discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d)))

SWU4

  inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0503/SWU4/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 2
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
## [1] "opening timeseries..."
  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal_overall, signal)
  ids_overall <- c(ids_overall, tsobj$dataset)

  cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/SWU4/FSL_frf_nsc_ngs_aal/'
  cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
  scan_pos = 2
  cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
## [1] "opening graphs..."
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  cpac_graphs <- cpac_graobj[[1]]
  cpac_ids <- cpac_graobj[[3]]
  
  cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
  ids_overall <- c(ids_overall, cpac_graobj$dataset)

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

CPAC Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)
## [1] "computing hellinger distances and densities..."

  print(td$combinedplot)
## NULL

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)
## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)
## NULL

CPAC Raw Correlation Graphs

  cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
## [1] "computing hellinger distances and densities..."

  print(cpac_td$combinedplot)
## NULL

CPAC Ranked Correlation Graphs

  cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
  print(cpac_tdr$combinedplot)

BNU2

  inpath <- 'C:/Users/ebrid/Documents/R/fngs_merge/BNU2/roi_timeseries/desikan-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 3
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)
  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal_overall, signal)
  ids_overall <- c(ids_overall, tsobj$dataset)

  cpac_inpath <- 'C:/Users/ebrid/Documents/R/CPAC_results/BNU2/FSL_frf_nsc_ngs_des/'
  cpac_tsnames <- list.files(cpac_inpath, pattern="\\.graphml", full.names=TRUE)
  scan_pos = 2
  cpac_graobj <- open_graphs(cpac_tsnames, sub_pos=scan_pos)
  cpac_graphs <- cpac_graobj[[1]]
  cpac_ids <- cpac_graobj[[3]]
  
  cpac_graphs_overall <- c(cpac_graphs_overall, cpac_graphs)
  ids_overall <- c(ids_overall, cpac_graobj$dataset)

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

CPAC Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(cpac_graphs[[1]], title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)
  print(td$combinedplot)

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)
  print(tdr$combinedplot)

CPAC Raw Correlation Graphs

  cpac_td <- time_discr(cpac_graphs, cpac_ids, rank=FALSE, graphs = TRUE)
  print(cpac_td$combinedplot)

CPAC Ranked Correlation Graphs

  cpac_tdr <- time_discr(cpac_graphs, cpac_ids, rank=TRUE, graphs = TRUE)
  print(cpac_tdr$combinedplot)
  collection <- rbind(collection, data.frame(dataset='HNU1',
                                             postprocessing=c('fngs_corr', 'fngs_rcorr',
                                                              'cpac_corr', 'cpac_rcorr'),
                           discr=c(td$d, tdr$d, cpac_td$d, cpac_tdr$d)))
  collection$dataset <- factor(collection$dataset)
  collection$postprocessing <- factor(collection$postprocessing)
  summaryfig_fng <- ggplot(collection, aes(x=postprocessing, y=discr, color=dataset)) +
    geom_point(size=4) +
    ggtitle('Comparing Discriminability over 4 reference datasets using different postprocessing techniques')
  print(summaryfig_fng)

  summaryfig_fng <- ggplot(collection, aes(x=postprocessing, y=discr, fill=postprocessing)) +
    geom_violin() +
    geom_boxplot(width=0.1) +
    ggtitle('Comparing Discriminability over 4 reference datasets using different postprocessing techniques')
  print(summaryfig_fng)